Instead of a default blacklist, a default whitelist might make more sense, while at the same time not sacrificing some of the useful comments. To be clear, it would not be much different from how it is presently. The flag option could get an overhaul so that when a user flags a post they should be given a choice to select the appropriate reason in a dropdown such as, 'negative comment', 'off-topic', etc. and based on the reason the comment could either be deleted, hidden or collapsed.
However, this could also be acheived without making any changes to the commenting system. If the objective is to bring down the number of negative comments, the flag option would probably help achieve that, and if it is to decrease the frequency of off-topic comments, a private messaging system might serve well as HN is not just a place for reading tech news, for many people it's also a place to network and connect with like-minded people.
If you do go ahead with this change (which seems likely), at the very least add an option for users to see pending comments if they choose to, as that only seems fair.